Prophecy
by johnliz4ever
Summary: Sequal to Aftermath. You'd think her leaving would end the problems, well they've only just begun. Slight crossover with SG1. JohnElizabeth.
1. Chapter 1

Disclaimer: Don't own Stargate Atlantis or SG1

Note: Thanks to everyone who reviewed Aftermath, this is the sequel; this takes place 6 years into the future. This first chapter will probably be the longest (I got carried away).

Spoilers: Up to and including Season 2 Atlantis and season 9 SG1

**

* * *

Earth **(6 and a half Years later)

The thunder clapped, the lightning struck and the rain fell on the roof above.

Elizabeth was wide-awake listening to the rain.

Thunder and lighting had always scared her as a little girl so it wasn't a surprise that it scared her now, although she hadn't heard anything this bad since the storm on Atlantis.

Atlantis, now there was something she thought about all the time. She missed it; she missed her friends.

When she arrived back on Earth it had took her a while to settle back into life on Earth, but she survived.

Jack offered her a job at the SGC as a negotiation consultant, which she took, and everyone had helped her, even Sam, which surprised her since the two were known to have differences, but it was nice to have a female friend around. The guys were great but there was nothing like girl talk to make problems go away.

Elizabeth remembered when she first arrived back at the SGC with Bree. The whole feeling had been surreal but Jack had been so supportive.

**:Flashback: **(6 and a half Years ago)

Jack watched as a container full of equipment followed by Elizabeth came through the event horizon, Elizabeth quickly looking back as if she'd made a mistake. Jack left the control room and entered the 'Gate room.

He was confused to why she was back and what the small bundle in her arms was.

"Dr Weir? What's going on?"

Elizabeth walked down the ramp slowly; as she got closer, he could see what was in her arms.

"General, we need to talk"

Jack nodded; he was shocked to say the least. Whatever she had to say would be good.

"You two go get checked out."

Elizabeth nodded and was escorted to the infirmary. As she walked past him, Jack could see the wetness on her cheeks. He'd question that later but first of all he need to check they were both okay.

* * *

Jack walked into the infirmary and saw Elizabeth sat on one of the beds with the baby in her arms as the doctor gently pushed a needle in the baby's arm. Jack was expecting the child to start screaming like Charlie had when he had his shots as a baby but instead the baby barely whimpered and snuggled into Elizabeth's chest. Jack stood amazed for a second. Getting shot in the arm with a needle made _him _cry. 

Jack sighed for a moment before walking over to Elizabeth and sitting next to her.

"What's happened Elizabeth?"

Elizabeth turned to face him before looking at Bree who was being taken from her by a nurse so she could be checked over. She watched as Bree was taken out of the room before turning back to Jack.

"She's mine…obviously. Something happened on Atlantis, there was a storm and during the storm a group of…enemies came, tried to seize the city. When they failed, they took myself and Dr McKay back to their home world as prisoners."

Jack could see the tears forming slowly in Elizabeth's eyes, threatening to escape but she pushed them back and continued.

"One of their Commanders…"

Elizabeth's tears began to fall freely and Jack wrapped his arm around her shoulders as he quickly realised what had happened to her.

Jack felt angry, disgusted, he didn't know where Elizabeth had found the strength to keep the child.

Elizabeth's buried herself into Jack's shoulder. Elizabeth had never broken down like this before, she knew what John would have done if she did. She knew he would try and destroy whoever caused the pain, in that case it would be Kolya but with Jack she knew he couldn't do anything even if he wanted to.

Jack rubbed her back gently.

"It's okay, you're okay"

Elizabeth pulled herself from his shoulder and smiled

"I'm sorry"

Jack shook his head.

"Don't you dare apologise. You've done nothing wrong."

Elizabeth nodded slowly and Jack pulled her back into a hug.

**:End of Flashback:**

Elizabeth had eventually told him the rest of the story, about her and John, about the attack on Gistorri and what Bree had in her.

Jack had been very concerned about what Bree carried inside of her but after a series of tests, he was happy that she was no danger to Earth.

In all honesty, Elizabeth had been worried that the Wraith would be able to track her, like they did when Teyla connected with them but she also knew that unless Bree connected to them first nothing would happen.

Elizabeth turned over and tried to go back to sleep but her mind was going a mile-a-minute, as per usual. She closed her eyes and sighed.

She was just about to bury her head into her pillow when she heard the bedroom door creak open and the sound of tiny feet running towards her.

"Mummy?"

Elizabeth slowly sat up and saw the outline of a small girl stood next to her bed.

Elizabeth picked her up quietly and kissed her forehead.

"What's wrong Bree?"

"I can't sleep Mummy"

The small girl whispered and snuggled into Elizabeth chest.

Elizabeth swung her legs off the side of her bed and stood up, securing the girl in her arms before walking out of the bedroom, down the stairs and into the kitchen.

She switched on the kitchen light and placed the girl onto a nearby chair.

In the light, Elizabeth could see how identical Bree's features where to her own.

Dark brown hair, which was long and slightly curly, emerald green eyes, so was a little small for her age but Elizabeth accounted that to her being premature.

There were also other features; little things she'd tried to convince herself weren't there, little things that had become more and more present in recent years. Thinks which reminded her of Kolya. Elizabeth was good at pretending not to notice, but how could she not.

The shape of her ears and nose was all Kolya. But she could never tell Bree, she didn't know about him, all Bree knew was that she had a father who loved her.

Elizabeth poured some milk into a glass and, after placing Bree back into her arms and sitting down, gave it to her daughter.

"Okay, why can't you sleep?"

Bree took small sips from the milk.

"It's too loud"

Elizabeth kissed the top of Bree's head

"The thunder?"

Bree nodded, placing the glass of milk onto the coffee table and snuggling into her mum again.

They'd always been close, but they were almost always on their own.

All they really had was each other.

Elizabeth smiled as she heard gentle rhythmical breathing coming from her daughter. Her eyes were closed and she was limp in Elizabeth's arms.

Elizabeth stood up gently, not wanting to wake Bree up and took her back into her bedroom.

She placed Bree gently on the little bed and brushed away her messy hair, placing a kiss on her forehead.

"Sweet dreams honey"

Elizabeth walked to the door and stood there for a moment watching her sleeping daughter before gently closing the door and walking back into her bedroom.

She slid onto the bed and sighed.

She really missed Atlantis, but she'd done what was necessary to ensure safety for her daughter.

* * *

Elizabeth rolled onto her stomach as the early morning sun shone through her window. 

Elizabeth was tempted to stay in bed for the rest of the day. But she couldn't today, today was an important day for Bree and Elizabeth had to go wake her up.

Elizabeth slipped on a robe and walked out of her bedroom and down the corridors to Bree's. She knocked on the door gently.

"Bree are you awoke honey?"

There was no answer so Elizabeth silently slipped into the room.

"Bree?"

When she walked in she saw the bed neatly made and the drapes open.

Elizabeth analysed the situation. Bree hated making her bed, never remembered to open the drapes and never got up early unless someone woke her up. That could only mean one thing.

Elizabeth closed the bedroom door and rushed down the stairs. When she was halfway down, she could smell the unmistakable aroma of bacon and sausage.

She walked down the final steps and turned into the open-plan kitchen.

She stood by the doorframe for a moment and smiled at what she saw.

Her daughter was in the living room playing while a man with black, unruly hair stood at the stove watching her and cooking.

Elizabeth walked up behind him, slipping her arms around his waist and resting her head on his back.

He turned round and smirked at her.

"Hey"

He kissed her deeply on the lips before snuggling his head in her the curve of her neck as he began to nibble at her collarbone.

"I thought you weren't getting home until tomorrow"

The man removed his head from her neck and smirked.

"We got back early this morning, Daniel pissed off some dignitary"

Elizabeth shook her head and sighed

"Another mess for me to clean up?"

The man nodded and kissed her again before looking over at Bree.

"Plus, didn't I say I'd be here for her birthday?"

He smirked and Elizabeth kissed him again.

"Yes you did. Thank you. You are such a good father John"

John nodded and kissed her again, with more passion and fire this time, they were only interrupted when John smelt burning coming from the bacon.

Elizabeth than left him to go get changed. She walked into the bedroom, slipped off her clothes and got into the shower.

She was only in a few minutes when someone wrapped their arms around her and began nibbling at her neck.

"John"

John shushed her and turned her to face him. He pulled her towards him and began to kiss her.

Elizabeth pulled away

"What about Bree?"

John smirked

"She's getting ready for school, which will take a while, now get back here"

Elizabeth smirked and kissed him again.

John's arrival back on Earth had been a surprise that morning but nothing like the arrival of him nearly 6 years previously.

**:Flashback: **(6 years ago)

Elizabeth watched as Bree slowly stood up and holding onto the edge of the couch, slowly took a few steps towards her.

Bree lightly fell to the floor and moved onto her knees to begin to crawl.  
Elizabeth loved watching how her daughter developed. She loved to see the little things she could learn.

Elizabeth smiled as Bree crawled onto her lap. Elizabeth picked her up and Bree began to moan, Elizabeth took this as a sign and placed her back on the floor.  
Now Bree could move around by herself she hated being carried anywhere and voiced it.

Elizabeth watched her for a little longer, thinking until a knock on the door broke her musing. Sighing Elizabeth picked up Bree, despite her protests and placed her back in the playpen before going to the door.

As she opened the door, she was shocked by who she saw standing there.

His black dishevelled hair was still the same. His gorgeous green eyes still stared deep into her soul making her feel safe and warm.

He still had stubble on his face that felt so good against her skin.

"John?"

John shifted nervously in the doorway and looked down for a moment before looking up at her and smirking at her.

"Hey"

His smirk was broken. It reflected how both of them felt.

They stood there looking at each other before John broke the silence

"It's kinda cold, can I come in?"

Elizabeth shook out of her musing, slightly embarrassed, and let him into the house, closing the door behind him.

Elizabeth led him down into the living room, totally forgetting Bree was in there.

When he entered the living room, his eyes went immediately to the playpen. He smiled and walked over to Bree.

"She's grown. Can I…?"

Elizabeth nodded; John leant over and picked up Bree. She started to squirm in his arms before settling.

"Hey, do you remember me?"

He gently ran his fingers through her dark brown, wispy hair.

Bree began to gurgle and she wrapped her hand around one of his fingers.

Elizabeth quietly watched them. Bree wouldn't be able to remember him from being away from him for so long but she did seem comfortable with him, like she always had.

Elizabeth smiled at how sweet it looked.

John turned to face her.

"I've missed you both"

Elizabeth looked down slightly

"Do you want a coffee or something?"

John nodded slightly

"Yeah sure"

Elizabeth nodded and disappeared into the kitchen to make coffee. As she was waiting for the coffee to brew, she leant against the kitchen cabinet.

She couldn't believe he was here, in her home.

* * *

Elizabeth walked back into the living room a few moments later, where John was still holding Bree. Elizabeth placed the coffee cup on the table and John smiled at her. 

"Thanks."

He paused for a few moments until the silence became unbearable.

"I think she remembers me."

Elizabeth smiled shyly

"Maybe"

John nodded and sat down next to her, with Bree still in his arms. He was stuck for something to say, which was a surprise since he'd spent the past two days making a big speech. He forgot what he had planned to say to her, so he spoke from the heart.

"How are you?"

Elizabeth smiled and took a sip from her coffee before responding.

"I'm…okay."

John nodded; he looked down at Bree.

"I…I suppose you already know this but Atlantis has a new commander."

Elizabeth nodded

"It wasn't my recommendation."

"I know; they had a full ZPM, that's how I got back here."

Elizabeth nodded sadly but out of his sight

"And one to get you back I assume."

John stood up and put Bree back into the playpen, despite her protests.

"No"

Elizabeth's head snapped up.

"What?"

John sat down next to her, taking her hand in his.

"There is no ZMP to get me back. I'm staying on Earth."

"Why?"

Elizabeth knew what answer she wanted to hear, but she also felt bad that John was giving up his life for her.

"Because I want to be with you and Bree. You've been gone 6 months and it's been unbearable. I wanted to come home. Elizabeth, I don't know if you still want to be with me or even if you've met someone else…"

"No"

Elizabeth quickly jumped in. John smiled.

"Maybe we could make it work"

Elizabeth nodded slightly before shaking her head

"I can't ask you to give up your life. You love Atlantis"

John shook his head

"No, I only came because you asked me. I only stayed there when you went because they needed me, now they don't. It's my decision. I'm staying on Earth, with you and Bree."

Elizabeth smiled slightly as John closed the distance and gently kissed her. The kiss of course was broken by the sound of Bree crying. He looked round at Bree than to Elizabeth.

"She still does that?"

Elizabeth smiled

"Apparently so"

Elizabeth barely had time to finish the sentence when John's lips attacked hers again. She ran her hands up to his neck on through his hair, before breaking the kiss and dropping her head in his neck.

She breathed in his sent, just to tell herself that he was really there and this wasn't a dream, like she'd had so many times.

"I've missed you John"

She kissed his neck before looking up at him, than at Bree.

"I better go sort her out"

John stopped her, standing up himself.

"Let me do it. I can still remember how to calm her down"

He walked over to the playpen and took her out, holding her tightly as if she would be snatched from him if he didn't.

Elizabeth watched in awe as John expertly calmed down her daughter.

**:End of Flashback:**

Elizabeth draped her arms around John's neck as he placed a final kiss on her neck and held her in his arms.

"I missed you"

Elizabeth smirked wickedly, her eyes glimmering

"I could tell"

John kissed her again, keeping his arms around her as Elizabeth swivelled round in them to face the shower and switch it off. John protested with a moan but followed her out of the shower all-the-same.

The two of them quickly got changed, knowing that Bree could burst into their room anytime.

As Elizabeth sat her dresser, putting on a necklace, Bree came into the room excitedly.

"Mummy, the party's tonight and everyone's going to be there…"

Elizabeth cut her off by placing her finger to Bree's lips. She then pulled her up onto her lap and started brushing her hair.

"I know honey and the sooner you let Daddy take you to school the sooner I can start setting up for the party."

For Bree's seventh birthday, they decided a party was in order. Of course what had started out as a family gathering with a few of Bree's friends had turned into the party of the year. There was going to be a barbeque, which of course Jack had insisted on organising, a bouncy castle and whatever John had ordered without telling her.

This was going to be a better party than originally because John was there. SG1 had been called on a week long mission which meant that John would have to miss the party because they couldn't reschedule everything so they were going to do a small family thing after he'd come back, but because Daniel pissed off that dignitary, it meant he could be there for her birthday, plus SG1 could come.

"Is Uncle Jack coming?"

Elizabeth smiled, Bree was smitten with Jack, she saw him as an uncle since she didn't have any proper ones.

"I doubt he'd miss your birthday."

Bree gleamed up at her mother until she was pulled upwards by two strong arms. John threw her into the air slightly, catching her almost immediately.

"Come on lets get you to school."

He lowered her down to Elizabeth so she could kiss her on the cheek.

"Have a good day at school"

John set Bree on the floor with an instruction for her to go get her things, when she left John bent down and kissed Elizabeth on the lips.

"I've got to go collect Bree's present. So I'll be back by lunch."

Elizabeth nodded and gave him another kiss.

"Okay."

John left the room, picking Bree and her bag up on the way out. Elizabeth walked with them to the door, where she watched them get into the car and drive away.

Elizabeth closed the door and looked around the room.

This was going to be a great day.

* * *

John arrived at the small elementary school and watched as Bree ran into the building. On the way, she met with the Principle who she smiled at before going into the school. 

John got back into his car and was about to drive away when there was a tap at his car window. John opened the window and smiled at the Principle.

"Principle McCann, what can I do for you?"

"Mr Sheppard, I would prefer if we could speak in my office."

John sighed, took the keys out of the ignition and followed the woman to her office.

She indicated for John to take a seat as she picked up a file.

"Mr Sheppard. I wanted to see you because some things have been brought to my attention that I need to inform you of."

John sighed; he had a fair idea what direction this conversation was going in.

"Bree has been in first grade for a few months now, but she's still having trouble adjusting, she's behind the other children"

John nodded

"She was a baby when we relocated to Colorado, it might have had a negative effect on her. She doesn't adjust well"

The Principle nodded.

"She also gets upset and aggressive when you're away"

John sighed

"Are you here to bust me about being a bad father? Look I know I'm away a lot of the time, but I do it because I love her and in the long run it keeps her safe. And sorry, I know my daughter and she's not aggressive. She just plays a little rough sometimes."

The Principle nodded and looked in the file.

"What I am more worried about is her tendency to talk to herself and play alone."

John shook his head

"Bree has lots of friends"

"I know, and that's what makes it so worrying. Bree is a bright child with good grades but she has quite an imagination"

John sighed

"Bree doesn't have any brothers, sisters or cousins. The only other children she knows go here. Bree doesn't talk to herself at home, she has an imagination, so what I do too. It's not a bad thing"

"Some of what she says is very advanced for her age, and some of it is extremely disturbing. She talks about mythical cities and Alien races."

John's head shot up.

"What does she say?"

McCann looked at the file she had in her hands.

"She talks about Aliens that can kill by 'sucking the life out of their prey' about a race known as the 'Genii' and how she's a part of them."

John faulted when he heard the name Genii.

"Does she speak about the people of the …Genii?"

McCann nodded

"In particular a man named 'Kolya, Acastus Kolya' she says that both you and her mother know him"

John sat silently before looking up at McCann.

"I have to take Bree home now"

McCann shook her head

"I'm afraid you can't"

John stood up

"She's my daughter and I'm taking her home"

McCann stood up facing him, a curious look on her face.

"Is there something I should know?"

John shook his head

"No, just send someone to go get her"

McCann sighed and slipped into the office next to hers to ask her secretary to send someone down for Bree, while she was gone John picked up the file on McCann's desk and slipped it into his coat before walking out of the office to wait for Bree,

* * *

John arrived back at the house, carrying Bree in his arms. When he walked into the main entrance, he set Bree down on the floor. 

"Go to your room, while I talk with Mummy okay?"

Bree nodded and walked up to her room, Elizabeth came over to him but before she could ask he stopped her, grabbed her hand and led her over to the sliding doors and out to the back yard.

Elizabeth stood in front of him.

"John, what's going on? Why isn't she in school?"

John didn't answer, he just handed Elizabeth the file and let her read it. Elizabeth stood entranced by the contents of the file. When she couldn't take anymore she looked up at John.

"It's impossible"

John shook his head

"Nothing is impossible"

"I've never mentioned the Genii or Atlantis to her. Nobody has. I don't even let her watched that Atlantis Disney film."

John nodded

"I know, I have a theory. The Wraith use their minds to connect with each other. We experienced it with Teyla. The Genii are part Wraith so they'll have that ability. What if they can connect to her? What if Kolya has been in contact with her all her life."

Elizabeth fell onto one of the picnic chairs behind her, burying her head in her hands.

"He knows where she is."

* * *

**  
SGC**

Elizabeth sat with Jack and John in the observation room watching as Dr Lam examined Bree. Both men could see the emotions that were running across Elizabeth's face. Both knew just how difficult this was for her.

John grabbed Elizabeth's hand and held it lightly.

"She'll be okay"

Elizabeth shook her head

"You don't know that. Kolya told us she was part of a plan. I should have known then that taking her wouldn't do anything. I should have known, I'm her mother and I didn't see it."

Jack placed his hand on Elizabeth's knee and looked at her.

"She'll be okay. She has never shown any signs of being physically effected by it. If the Genii can contact her, it's obvious they can't hurt her."

Elizabeth shook her head, stood up and walked over to the viewing glass.

"He'd never hurt her, he loves her. She's his daughter"

Jack saw John falter when Elizabeth said that. Jack knew how John hated the reminder about who Bree really was, because he loved her so much, even though she wasn't his.

John stood up and walked over to Elizabeth wrapping his arms around her and resting his head in the crook of her neck.

"She'll be okay"

Elizabeth nodded slowly but both men could see her reflection in the glass, they could see the tears rolling down her cheeks.

* * *

An hour later Jack, John and Elizabeth watched as Dr Lam left the quarantine room, a few moments later she walked into the viewing room and went straight over to Elizabeth. 

"I can't find anything physically wrong with her; she's a healthy little girl. If they are connecting with her, it isn't harming her"

Elizabeth nodded slightly relieved but not completely.

"Did she talk to you about…?"

Dr Lam shook her head

"No…but she might be more responsive if you…"

Elizabeth understood what she was asking and Elizabeth nodded

"I'll do it."

Elizabeth followed Dr Lam down to the quarantine room. She took a seat next to Bree's bed, aware that Jack and John would hear everything she was about to say.

Bree looked up at her smiling but in confusion.

"Why am I here?"

Elizabeth gently lifted her daughter off the bed and placed her in her lap, wrapping the covers around her and running her fingers though Bree's hair.

"Honey, have you been talking to my friend Kolya?"

Bree looked down nervously.

"Honey it's okay. I'm not mad. Just tell me."

Bree looked up at her, fear in her eyes

"I'm not allowed to tell you. He said you and Daddy would be mad if I did. He said he was a secret."

Elizabeth nodded.

"Is he there now?"

Bree shook her head.

"He went away"

Elizabeth nodded again, she was about to ask Bree another question when she started to convulse in her arms.

"Bree?"

Dr Lam rushed over taking Bree out of Elizabeth's arms and pushing her to one side.

John rushed down from the viewing room and straight over to Elizabeth, holding her in his arms as her eyes stayed fixed on Bree.

A few moments later Elizabeth heard a small voice calling her name.

"My dear Elizabeth"

Dr Lam jumped back from Bree as she heard her speak. Elizabeth pulled herself from John's arms and went over to where Bree was laying.

"Bree?"

Bree shook her head and smiled wickedly

"No. She's here but right now I want to speak with you"

Elizabeth shuddered at how cold the voice sounded

"Kolya?"

Bree nodded

"They are so easy to manipulate at this age, so innocent. I've been with Bree since she was born. I've always been here with her in her mind. I can see what she sees. My plan was to take her home with me on Gistorri but what I didn't factor was your suspicion of Jota. I guess I should have, you've always been super observant."

Bree turned and looked at John

"Colonel Sheppard, a pleasure to see you, as always. She knows that I'm her father and you're nothing."

John clenched his fists

"Shut up"

Bree smirked

"You can't save her from her destiny, it's prophesied. But she will need help in controlling herself, things will guess worse for Bree and I'm the only one who can help."

Bree turned back to Elizabeth

"I think you know what you have to do. So long my sweet"

Bree's head fell back down onto the pillow behind her, after a moment she slowly raised her head and looked at Elizabeth

"Mummy, what happened?"

Her eyes were full of tears, matching Elizabeths. Elizabeth walked over to her and kissed her forehead tenderly.

"You're okay now sweetheart, you're okay"

Elizabeth looked back at John, tears now falling freely from her eyes.

* * *

Elizabeth, John, Jack, Dr Lam and SG1 sat around the briefing room table. Elizabeth would have preferred to keep SG1 away but once Daniel had found out what had happened there was no chance of that happening. 

Jack looked at Elizabeth.

"Elizabeth any thoughts? You know Kolya better than anyone. What does he want?"

Elizabeth sighed and looked down.

"He wants me and Bree. I'm pretty sure he wants us to go back to Atlantis and contact him through the Genii. Then we'll probably meet at a neutral planet and then he will want to go to Atlantis. And my guess is he'll use Bree to get all that"

John shook his head

"Not if we don't let him. This is bait and we won't bite."

Elizabeth sighed and shook her head.

"You saw what he did to her. He'll keep doing that until we comply. He isn't doing it to hurt her; he's doing it to hurt us."

John shook his head

"We should think about this"

Elizabeth shook her head

"I've made up my mind. The only way to end this is to meet with him."

John stared at her

"I don't get a say?"

Elizabeth shook her head sadly, regret in her eyes

"I'm sorry John. But this is my decision to make."

John stood up and held the table tightly. He looked like he was about to say something but instead he stormed out of the briefing room.

* * *

John stormed into the gym and straight over to the punch bag and began to beat the hell out of it. He couldn't believe Elizabeth could be so heartless, that she could say that. 

He didn't want it to be true but it seemed like his father might have been right.

**:Flashback: **(5 and a half years ago)

Five months after John had come back to Earth and got settled with Elizabeth and Bree, Elizabeth had suggested meeting his parents. Elizabeth's parents had died when she was young and John knew how much Elizabeth wanted Bree to have grandparents so John had agreed to contact his parents and invite them to dinner so Elizabeth could meet them.

That dinner was tonight.

Elizabeth was in the kitchen finishing dinner while John was in the bedroom getting changed, he stepped out and walked down the stairs into the kitchen. Elizabeth turned round when John stepped into the kitchen and swooned at him.

"Nice."

John was wearing a simple black shirt with a few buttons at the top undone and some black trousers.

Elizabeth walked over to him, slipping her arms around his waist and kissing him.

"Thank you for doing this."

John nodded and kissed the top of her head before looking at what she was wearing.

It was a simple black strappy dress with cross-stitch detail trim, which hung to her figure perfectly. The shoes were strappy black heels, which complimented the dress perfectly.

John lowered his head and whispered into her ear.

"You look so beautiful"

Elizabeth blushed slightly before stepping away from him.

"Thank you"

Elizabeth turned back to the stove and John went into the living room and picked up Bree.

Bree flapped her arms as he picked her up.

"Da da"

Bree was about 15 months now, she was starting to communicate with them, and as far as she was concerned, he was a Dad.

He kissed her forehead and sat down with her and his lap, gently rocking her until he heard a knock on the door. John stood up nervously and he saw Elizabeth walking to the door.

"No, let me."

Elizabeth nodded understanding that it had to be John who let them back into his life.

John handed Bree to Elizabeth and opened the door to find a man and a woman standing there.

The man was about six foot, husky and Elizabeth could finally see where John got the bed head hair from. The woman was slightly smaller than the man, with dark brown hair with freckled grey patches.

When the woman saw John, she wrapped her arms around him affectionately and held him in a long hug.

"John darling, it is good to see you again"

She pulled away from him and Elizabeth could see the tears, which were falling down the woman's cheeks. John then turned to the man next to her; he took a sharp intake of breath.

"Dad."

The man nodded

"John"

John ushered them into the house and down to the living room before grabbing Elizabeth's free hand and walking to join them.

The four adults stood nervously waiting for the tension to break. After a moment, John broke the silence

"Okay, Elizabeth this is my mum Julianne and my dad Trevor"

Elizabeth smiled politely and shook their hands with her free hand.

"Mum, Dad this is Elizabeth and our little terror Bree"

His parents nodded before his Dad turned to Elizabeth.

"How old is she?"

Elizabeth thought for a moment before responding

"About 15 months"

Trevor nodded, shocked

"15 months?" He turned and looked at John "Were the two of you away on deployment?"

John looked away and Elizabeth quickly stepped in.

"We were out of the country when she was born. John and I met in Antarctica, I was there negotiating a land treaty and John was one of the pilots flying people back and forth. We met and then I was called away again, long story short I needed a pilot and I asked John. The rest is history."

Julianne nodded.

"When did you both get back?"

Elizabeth hesitated and John jumped in

"About 5 months ago. We both agreed we wanted Bree to grow up in America"

His parents nodded and let the subject drop.

Elizabeth saw Julianne looking at Bree

"Would you like to hold her?"

Julianne smiled at Elizabeth and took Bree from her hands.

"She's so small, was she…?"

Elizabeth nodded

"She was a month premature"

Julianne continued to dote over her 'granddaughter' and Elizabeth disappeared into the kitchen with John.

Elizabeth grabbed his hands and held them.

"They know we fed them a lie, don't they?"

John nodded

"My Dad knows, but my Mum will choose to ignore it"

Elizabeth nodded and took out some wine while John got some beers and they took them back out into the living room.

Julianne looked at the two returning adults

"She's so beautiful; she seems to take after you Elizabeth"

Elizabeth nodded while John distributed the drinks.

Elizabeth saw Bree yawn and snuggle into Julianne's chest.

"I better put her to bed"

Julianne handed Bree over to Elizabeth; she looked over at her husband and sensed that he wanted to talk to John alone.

"I'll help you"

The two women disappeared up the stairs to Bree's room. John looked at his father before picking up one of the wine glasses and having a sip. He looked back up at his father and saw him staring.

John sighed and sat down on the couch

"Say it"

Trevor shook his head

"Say what?"

John stared at him, not amused.

"Say whatever the hell you are dying to say"

Trevor sat down next to him and picked up one of the beers.

"Well first of all, I know you're lying, and so is Elizabeth. Classified mission I get that. But not even you, my boy, would be stupid enough to knock up your superior, because that is what she was, isn't that true?"

John just took another sip from his wine and avoided his father's eyes.

"It doesn't matter who Bree's biological father is because I'm the one that's here now"

Trevor laughed at how pathetic his son sounded.

"Until he comes back, that watch what happens"

John shook his head.

"He's not coming back; he's never getting anywhere near Elizabeth or Bree again"

Trevor made John face him

"Tell yourself that now son, but when it comes to choosing, she will pick what is best for her daughter and you will not get a say"

John tore away from his father and stood up.

"Elizabeth never wants to see him again"

"How can you be so sure?"

"Because he…" John stopped and looked away from his father "…It's none of your business Dad,"

Trevor walked over to him

"What did he do? Cheat on her, leave her when he found out she was pregnant? Come on what did he do?"

John snapped and looked at his father

"He raped her"

John immediately regretted it and his father could tell.

"Forget I said anything"

John walked over to the sliding doors and pressed his forehead against the glass, his father walked over to him, placing his hands on his shoulders and forcing John to face him.

"What happened John?"

John tried to escape from his father but he kept a hold on his shoulders fixing him in one place.

"Tell me."

John looked down before looking back up at him.

"Obviously we were on a classified mission. There was a situation on the base, Elizabeth and a scientist were taken hostage and then abducted. About seven months later, my team stormed the base they were taken. We found the scientist, relatively unharmed. He'd been helping them in exchange for keeping Elizabeth safety. When she found Elizabeth…it was…difficult, she'd been put under all sorts of torture, it resulted in Stockholm syndrome, but it didn't end there. They 'brainwashed' her, made her believe she was married to the bastard that raped her. It was rape; she didn't know who she was. Eventually I managed to bring her back, but by then she was already pregnant, she wasn't even far gone. Just a couple of days. When I found out, two months later and she told me she was keeping the baby; I was so mad with her, I wanted to hate her but I couldn't. I eventually came round to the idea, the day Bree was born. Elizabeth took one look at her and was terrified. I took Bree that day and I remember when I first looked at her, all I could see was Elizabeth, her hair, her eyes, her beauty. So that's it, that's everything"

His father, who had been watching John's face during the whole thing, pulled his son into a hug.

"You've never properly let yourself think about it. Never gone through in your head"

John shook his head.

"I always think about what happened to Mum when I do"

Trevor nodded

"I know."

**:End of flashback:**

John's father had been there for John since he told him the truth but one thing he said always played in John's mind

"_Tell yourself that now son, but when it comes to choosing, she will pick what is best for her daughter and you will not get a say"_

He never believed his father would be right about that, but seemed to be playing out, seemed to be happening. She was choosing to go see Kolya and he didn't get a say.

John sighed as he heard the door to the gym open. He expected it to be Jack, scolding him for being an ass, but instead it was Daniel.

"How did you find me?"

"We've been friends for over 4 years; I think I know by now where you go when you need to blow off a little steam"

John nodded

"Is Elizabeth okay?"

Daniel nodded and walked over to him

"She was a little upset, but she's okay now. Jack's with her"

John nodded

"I'm afraid, it's stupid but I'm afraid she'll go back to him."

Daniel shook his head

"You need your head examining if you think that. She hates Kolya and she is head over heels in love with you, just like you are with her."

John moved over to one of the benches and sat down.

"I know all that. I do and I'm still scared."

Daniel sat next to him, placing a hand on his shoulder.

"At the end of the day, you need to do what is best for Bree. If he can help her, isn't that what counts?"

John nodded slowly and looked up at Daniel

"Thanks"

Daniel nodded

"No problem"

John stood up and left the gym, he walked down to the infirmary where they were now keeping Bree. He walked in and saw Elizabeth sat next to Bree's bed alone.

He walked up behind her, placing a kiss on her head before sighing.

"We'll do it."

**SGC **(Several weeks later)

Elizabeth stood at the bottom of the Stargate ramp, looking up at the big metallic structure. Thanks to a power loop interface, Sam was able to generate enough power from an almost depilated Mark II naquadah generator to power the Stargate to the Pegasus galaxy several times.

One was used to make sure the Atlantis crew were still there, inform them of the situation and request permission for a small number of people to go through.

The second was going to be used to send John, Elizabeth and Bree through the Stargate. Jack had suggested sending a team just in case but Elizabeth had told him that without any means to get back to Earth the team would be stuck there. Jack reluctantly agreed not to send a team through with them.

Jack walked over to Elizabeth and stood next to her.

"Today's the day"

Elizabeth nodded and Jack sighed

"SG1 are prepped and ready to go, if you want them with you"

Elizabeth shook her head

"I have always had faith in my flagship team. That's why I allowed John to pick them."

Jack nodded

"I think Daniel really wants to go with the three of you."

Elizabeth turned to face Jack

"You need him here"

It wasn't a question, it was a statement. Earth needed SG1; they were already going to be missing John. They couldn't afford to lose anyone else."

Jack nodded

"Well, once you're ready, we'll start the dialling sequence"

Elizabeth nodded and the two of them walked up to the control room where SG1, John and Bree were.

Daniel walked over to Elizabeth and wrapped her in a hug.

"Be safe out there"

Elizabeth nodded

"We will be"

After a few more goodbyes to the rest of the team and Jack, John, Elizabeth and Bree walked down to the 'Gate room.

They had told Bree they were going on a trip.

And it was going to be one hell of a trip.

TBC…


	2. Chapter 2

Disclaimer: I don't own Stargate Atlantis.

Note: Sorry it's been a while but I had my GCSEs to revise for and do but now I'm all done which should mean more updates. Thanks to everyone who reviewed.

**

* * *

Atlantis**

Elizabeth, John and Bree emerged in Atlantis only a few seconds after leaving Earth. It was impossible to prepare Bree for the trip and she did seem very shaken by the whole thing.

Elizabeth turned to her daughter and bent down, wrapping her arms around her.

"Are you okay honey?"

Bree nodded and quickly snuggled into her mother as two men approached them. Elizabeth looked up and smiled at the familiar faces of Aiden and Carson.

She turned back to Bree and spoke in a soft tone.

"Honey, these are my friends. This is Aiden…" she told her gesturing to Aiden "…and this is Carson"

Carson bent down in front of her and smiled.

"You don't remember me do you? Well that's okay but I need to make sure you're okay after your trip"

Bree looked nervously between her mother and Carson. Elizabeth nodded

"It's okay. Carson will look after you."

Carson held out his hand and Bree slowly took it. Carson lifted Bree into his arms and held her gently. He turned to Elizabeth and John.

"It's good to see you both again. We'll be in the infirmary"

Elizabeth smiled at him and watched as he carried Bree out of her sight.

She than turned her attention back towards Aiden and a man who was approaching them. He was obviously the Atlantis commander now. He smiled at her, though she suspected it was a fake smiled.

"Dr Elizabeth Weir, it's so good to finally meet you. I'm Colonel Steven Caldwell."

Elizabeth smiled politely but couldn't help but feel that he wanted her off his city as quickly as possible.

Caldwell than turned to John.

"Colonel Sheppard, it's good to see you again"

John put on his typical 'don't give me that shit' smile.

"Good to see you again too Sir"

Caldwell saw the smiled and glared at him before turning back to Elizabeth and smiling.

"We have done what was requested. The Genii have been contacted and they agreed to the terms we laid out. Our security team will meet Kolya and his security team on an unpopulated planet, we'll check them for weapons and once they are given the all clear we will bring them back to Atlantis. But there's one thing, to make sure we are not springing a trap they want you to go to the planet Dr Weir."

Elizabeth looked down. She was not all too happy about seeing Kolya again but she couldn't bare to see him any earlier than she had too, but there was no other option.

"Okay, if that's their only term, I'll go"

John was about to object when he stopped

"_Tell yourself that now son, but when it comes to choosing, she will pick what is best for her daughter and you will not get a say"_

Those words rang through his head again, words that were so harsh but so true.

Aiden saw the change in his friend's posture, he saw the look on his face and realised that John didn't support the course of action they were taking. Aiden sighed inwardly.

Caldwell led Elizabeth up to his office so he could go into details about the meet. Aiden and John stood awkwardly for a few moments before John spoke.

"So…how…how are McKay and Teyla?"

Aiden nodded and they began to walk away from the control room and down to the infirmary

"They're okay, Teyla's on the mainland at the minute, I think McKay is in his lab."

John stopped and turned to his friend

"What happened?"

Ford faced his CO and sighed

"We had a small disagreement concerning…well contacting Kolya. McKay…he was adamant he didn't want him anywhere near Atlantis, Bree or Dr Weir."

John nodded

"That's kinda where I stand"

Aiden nodded and carried on walking

"I could tell, I thought that if Kolya can help Bree, why not let him."

John sighed

"That's exactly what Elizabeth thought"

John ran to catch up with Aiden; he still hadn't mentioned Teyla's position on the disagreement

"What did Teyla say?"

Aiden kept on walking, sighing and shaking his head

"She didn't think it was her place to say whether we should decide or not… she got angry at us because we were more concerned with being right instead of what was right for Bree"

John nodded slightly

"She's right, we have all been thinking about ourselves. I didn't want to see him again but…that not necessarily what's right for Bree."

Aiden sighed and thought it would be better to change the subject. He smiled smugly and turned to John.

"Sooo…did you make an honest woman out of her?"

John turned round to him, smiling and shaking his head

"No. Elizabeth and I are quite happy the way we are. A piece of paper isn't anything special. It's the feeling that matter"

Aiden smiled and laughed

"When did you get sappy?"

John smiled

"I've always been sappy Aiden; I've just never shown it"

The two men laughed lightly.

"I've missed this. Don't get me wrong, SG1 and Jack are great but…I've missed this, cut off from rules and regulations, able to have a laugh and not after to look over your shoulder to make sure there's no General you're going to offend"

Aiden sighed when he saw the look in his friend's eyes

"Do you regret going back to Earth?"

John shook his head

"No, I made that decision because that was what I wanted, what I still want. I just sometimes miss the city and everyone on it. Elizabeth is the same way, but we don't let it get us down"

Aiden nodded and the two friends stayed silent until they reached the infirmary where Bree was sat on one of the far beds playing with Carson's Stethoscope.

John walked over to the bed, picked her up in his arms, and tickled her causing her to laugh uncontrollably.

Aiden watched them with sadness. He knew how much John wished Bree were his, Aiden knew how much it killed him that she wasn't

**Flashback **(6 and a half years ago)

The team watched as Elizabeth stepped though the Stargate with Bree in her arms.

As the Stargate shutdown their eyes dropped to the ground and Rodney was the first to break the silence

"Well I…I guess that's it then"

He rushed out of the 'Gate room but not quick enough because they all heard the sobs cracking his voice. Teyla shook her head sadly and went after the scientist to check he was okay.

As the rest dispersed, Aiden kept watching John who was staring at the Stargate as if he was in a trance. Slowly Aiden walked over to him

"Sir"

John completely blanked him and walked out to the balcony, ignoring the concerned looks from the crew. Aiden thought for a minute. Maybe he should leave him alone to get it out of his system. Aiden shook his head. John needed his support and he'd be there to give it.

Aiden slowly made his way out onto the balcony. When he stepped outside, he could see John gripping so hard on the railing that his knuckles were turning white.

He didn't think John had noticed he was there, he was about to say something when John spoke.

"It's not fair; this damn fuck up situation is not fair. We didn't do anything wrong and we're being punished."

Aiden slowly walked to stand next to him; Aiden rested his hands on the railing and sighed

"I know Sir. None of you deserve this"

John pulled on of his hands of the railings to wipe his eyes but it did no good, the tears were simply replaced by more.

"I want Bree to be mine so much it hurts. I think that if we could just pretend that she was mine…it would be easier…but he would still be there wouldn't he? Haunting us, making our lives a living hell. I just want to kill the bastard and get it over with, but I can't because I would be killing a part of Bree and she as done nothing wrong."

Aiden nodded

"I know Sir"

John turned to face Aiden briefly before looking back out to the ocean.

"She must think I hate her…for going, like she thought I hated her for going through with the pregnancy and having Bree, she must think I'm a right bastard"

Aiden quickly shook his head and reassured him

"That is not true Sir and I know that for a fact"

John looked at Aiden sceptically

"How in the world could you know that Aiden?"

Aiden sighed and looked out across the ocean

"When she was pregnant she became increasingly paranoid"

Aiden laughed slightly at the memory before continuing

"There were rumours going around that you were seeing someone on the mainland. I told her it wasn't true, she said she wouldn't blame you if you were. But she never once said she hated you or that she thought any less of you. She said that she wanted you to be happy"

John closed his eyes

"I was happy with them. I love them both…so much. I should have told her but…it would have made things more difficult. All I want now is to hold them in my arms, but it's too late."

**End of Flashback **

It might have happened over six years ago but Aiden still remembered that day so clearly it hurt and watching them now just brought it home to him how difficult these next few days would be and he just hoped they'd all be able to handle it.

TBC…


	3. Chapter 3

Disclaimer: I don't own Stargate Atlantis, if I did I would be one very happy girl.

Note: Thanks so much for the reviews; I'm glad you're enjoying this.

* * *

Elizabeth stood at the doorway watching John with _his _daughter and it ripped her heart in two.  
She knew how much John loved Bree and how much it would hurt him to see Kolya again. 

She wasn't stupid, but she also wasn't going to risk Bree's life, she didn't know what was happening to Bree, nobody knew. The only person who did who did know how to help her was Kolya.

She sighed and walked over to were John and Bree were.  
She slowly sat next to him without a word.

When John heard Elizabeth sit down he looked round to face her.  
She was wearing a combat vest and clearly ready to go with Bates and his team to meet Kolya.  
John stood up and look Elizabeth's hand, forcing her to stand up and follow him, leaving Bree with Aiden.

John dragged Elizabeth over to the far corner of the infirmary, still holding her hand.

"Are you sure you don't want me to come with you?"

Elizabeth nodded and squeezed his hand.

"One of us needs to stay with Bree, I'll be fine."

John nodded and lightly kissed her forehead.

"Be careful, if something doesn't feel right get the hell out of there."

"I'll be okay, he won't hurt me."

John nodded slowly, he knew Kolya wouldn't hurt Elizabeth and on some level that scared him because it kept reminding him how much Kolya actually loved Elizabeth and Bree.  
Slowly Elizabeth kissed his cheek before walking over to Bree and hugging her tightly.

John watched as Elizabeth left the infirmary before going over to Bree and taking her in his arms, holding her tightly.

* * *

**Off world **(Kora)

Elizabeth stepped out of the Stargate on the planet of Kora, the planet agreed to by both Atlantis and the Genii as the meeting place between their teams.

To say she was nervous was an understatement. She was terrified, she hadn't seen Kolya in 6 years, but he'd obviously been keeping track of her.

She shook her head trying to get away from the unsure feelings she was having.

Bates, noticing Elizabeth's uneasiness placed a hand on her shoulder

"Dr Weir…"

She turned to him

"I'm fine."

Bates nodded and the two of them walked, with the team, where an area where the security had already secured and where Kolya was waiting for them.

As she neared the area, Elizabeth could see him clearer and clearer. Her chest started closing and she thought she was going to collapse. Bates saw her pale and grabbed her arm quickly.

"Breathe, just breathe. I won't let him touch you"

Elizabeth nodded slightly.

Bates might be a lot of things but heartless isn't one of them, he remembered how Elizabeth was after the incident on Gistorri, he knew how much the rape had effected her, he knew a piece of her had been lost. He could tell that she had slowly repaired since being on Earth but he knew she was completely healed.

As they stepped into Kolya's view Bates could see a smirk form across his face causing Bates to have to push down the desire to punch Kolya out.

Elizabeth pulled away from Bates and he understood her reasoning. She didn't want to show weakness in front of Kolya, she didn't want him to know that he'd gotten to her.

Elizabeth and Bates finally stopped a few feet in front of Kolya and his two guards, behind them was stood the Atlantis security.

When Kolya took a step forward Bates raised his gun, causing Kolya's guards to raise their guns, which in turn meant that the security team lifted their guns.

Kolya head up his hands and his guards slowly lowered their guns.

"Let's start how we mean to go on. Peaceful"

Elizabeth glanced at Bates; he quickly understood and lowered his gun, followed by his security team. He saw her stare at Kolya for a moment, as if trying to figure out his endgame.

"Elizabeth, I can't begin to tell you how good it is to see you again"

Elizabeth shook her head

"I wish I could say the feeling is mutual, but I'd be lying."

Kolya chuckled slightly.

"That's what I like about you Elizabeth"

Elizabeth glared at him before steadying herself,

"Can you help _my _daughter, because if you can't we are leaving right now"

Kolya smiled

"I would not have brought you here if I could not deliver on a promise. I will not let any harm come to _our _daughter."

Elizabeth shuddered at his words.

"Fine, but we get any indication…"

Kolya cut her off

"…Me and my men have no intention of betraying you"

Bates rolled his eyes when he heard that but it was Elizabeth who came up with the retort.

"I recall you people have said something like that before"

Kolya nodded in agreement.

"That is true, but I am not here on behalf of the Genii and neither are my men. We are here to help Bree"

Elizabeth nodded slowly before taking a commanding tone in her voice

"Well, just remember that we play by my rules, you want to see Bree and I want you to help her, that's where it ends"

Kolya nodded

"Agreed"

* * *

**Atlantis**

John sat in the infirmary with Bree in his arms; she was currently playing with his hair making it more dishevelled then usual. John knew that in a few moments everything would change, Bree would finally have to learn everything, and that scared him.

He didn't want Bree to know the real reason she was there. No child should have to know that they are the result of rape.

John knew all too well what that could do to a child. His mother had been raped, she'd fallen pregnant because of it, she kept the child and that child was him.

That's why he'd been so angry when he found out that Elizabeth was pregnant, he knew how Bree would feel if and when she ever found out. Even though Trevor had always treated him as his son, John knew he wasn't and always strived to make his 'dad' proud of him.

John had found out when he was only ten, quite by accident really. Something was said that shouldn't have been said, John had figured out that his dad really wasn't his dad.

He remembered his mother, how she told him the truth with tears streaming from her eyes. John had been unable to fully grasp what had happened to his mother and he'd runaway, only for a day, to his friends house where his friend hid him.

One thing John had always been curious about was who his real father was. He knew it sounded crazy but he'd always wanted to meet him, demand an explanation and then punch him out.

He'd never told Elizabeth, couldn't even think about how she would look at him if she ever found out.

There were some days when he just wished that his mother had an abortion, and he knew that if Bree ever found out about herself, that she'd wish it too.

Slowly John was brought out of his musing as Carson walked over to him.

"John, Caldwell as just informed that they are here"

John nodded and lifted Bree up onto the bed.

"Honey, you need to go to sleep for a little while. I'll be here when you wake up."

Bree nodded and Carson slowly injected her with a sedative and she quickly fell asleep.

One thing John had insisted on and Elizabeth had agreed to, was that if Kolya actually wanted to meet her straightaway, she would be unconscious. They hadn't really prepared her for what was about to happen and they needed to.

John sat watching his daughter for a few more minutes until he heard the infirmary doors open. He knew it was Kolya but he didn't want to turn round, didn't want to face him, but he knew he had to.

Slowly John turned to him, he had two guards either side of him and a group of Atlantis guards around them.

Elizabeth walked though the door with Bates who had a pissed off look in his eyes. Obviously, he was as unhappy about this as John was.

"Colonel Sheppard, how good it is to see you again"

John shook his head

"I'd say it's a pleasure, but my mother taught me not to lie"

Kolya smirked and looked at Elizabeth

"He's obviously rubbing off on you. You've developed a similar sense of humour."

Kolya looked like he was about to say more when his eyes spotted the bed and the small girl laying in it.

He slowly took a step forward.

"Is that her?"

Elizabeth nodded slowly and Kolya smiled. Even though it was suppose to be a happy smile it still gave both John and Elizabeth an uneasy feeling.

"She is beautiful"

Kolya examined the delicate details of her face; she was everything he'd imagined she would be and more. Kolya was overcome by so many feelings, but the main feeling was love. Love for this little girl, _his_ little girl.

"I want to hold her"

Elizabeth shook her head almost immediately

"Absolutely not"

Kolya turned to her sharply

"Do you want me to help her or not?"

Kolya knew trying that was a long shot. He wanted to help Bree desperately, he could help her control what was going to happen, but at the minute the knowledge he had was his only card, and he was going to use that all he could.

Elizabeth thought for a minute, Kolya was a bastard, he was evil but he could help her daughter. Part of her wondered whether he would just let Bree die, she didn't want to take that risk.

She looked at John apologetically before looking back at Kolya

"Fine, but only for a moment"

John clenched his fists in anger but knew there was nothing he could do. He watched as Elizabeth walked past him and picked up Bree who was still sleeping soundly. She then walked over to Kolya and, quite reluctantly, handed her to him.

That was enough to piss off John but instead he took a deep breath and mentally shook himself. It was all for Bree after all.

When Bree was placed in his arms, Kolya kissed her gently on the forehead before drawing a finger down her cheek in an attempt to wake her up, not knowing that she had been sedated.

"Why will she not wake up?"

Elizabeth sighed

"She as been sedated, did you think I was going to let her be awoke the first time you met her?"

John took pleasure as he saw Kolya look very pissed off.

"You promised me a chance to see _my _daughter"

Elizabeth nodded

"And you have seen her, but I still need a chance to prepare her, until I do that, she will not meet you"

Kolya shook his head

"She already know about me"

Elizabeth didn't answer, instead she just took Bree from his arms and gave her to John, who automatically held her tightly and placed a gentle kiss to her forehead.

Kolya sharply looked at Elizabeth

"Anymore deceit and I will not help her"

Elizabeth nodded

"Fine"

She then turned to Bates who nodded and turned to Kolya.

"You will be taken to your temporary quarters now"

Caldwell had agreed that locking Kolya and his men in a cell might not be the best way to get Kolya to help, so instead he'd agreed to place them in a secluded part of the city with armed guards everywhere.

As Kolya left Elizabeth walked over to John, who placed Bree gently on the bed.

John was unsure about what Elizabeth was going to do, until she wrapped her arms around him tightly and hugged him.

John slowly slid his arms around her and held her.

TBC…


	4. Chapter 4

Disclaimer: Not mine 

Note: This has a lot of experimental stuff in so I hope it works out okay.

Elizabeth laid on her side as she brushed her daughters hair from her forehead. Carson had allowed to Elizabeth to take Bree out of the infirmary so she had taken her daughter to her quarters where she had fallen back to sleep. Elizabeth placed a gentle kiss to Bree's temple before laying her head next to Bree's and closing her eyes. She didn't want to leave Bree, not while Kolya was on the city.

Quietly she heard the door open, quickly she looked round, fearing that it might be Kolya, instead it was John. Elizabeth breathed a sigh of relief has he walked over to them and lied next to Elizabeth on the bed, his hand resting on her upper thigh.

"Hey, how's she doing?"

Elizabeth sighed

"She's tired, she's had a long day"

John nodded and kissed Elizabeth's cheek

"So have you. You should try to get some sleep"

Elizabeth shook her head

"I don't think I can"

Elizabeth ran her fingers through Bree's hair

"I keep thinking that I'll wake up and she'll be gone, that Kolya will have her"

John wrapped his arm around Elizabeth's waist and held her tight, he stretched his free hand over to Bree and held her small hand which unconsciously grabbed John's tightly in a grip which was difficult for him to break out of.

"I won't let anything happen to either of you. I'll never let him hurt either of you."

Elizabeth turned round and kissed him.

"You promise?"

John nodded

"I promise"

_Elizabeth woke up the next morning with one hand resting on her waist and one stroking through her hair while in her arms were wrapped around their beautiful daughter. _

_Elizabeth slowly took the hand which was sitting on her waist and brought it up to her lips, kissing it delicately._

_Elizabeth couldn't believe how incredibly safe she felt. Slowly she looked around the room taking a second to recognize her surroundings. Something wasn't right. _

_They weren't in Atlantis. Everything about the room told her that they weren't on Earth either. The room was so familiar but she couldn't place where she'd seen it before. _

_Slowly she felt the person next to her leave the bed and slip into the next room. She turned round quickly but only saw the door closing. Listening she heard the shower switch on. _

_Elizabeth slipped out of the bed trying not to disturb her daughter. Quickly she walked over to the window and opened the curtains. On opening the curtains, what she saw shocked her. Outside was lots of small wooden houses and people walking around in clothes which reminding Elizabeth of her 16th century English history class. _

_Elizabeth stayed at the window in shock until she felt someone grab onto her leg._

"_Momma"_

_Elizabeth looked down and saw a head of disheveled hair clinging to her._

_The child looked up at her. _

"_Momma, are you okay?"_

_Elizabeth stepped back from the child. _

"_Bree?"_

_The girl nodded, dropping her grip from Elizabeth. Elizabeth jumped back in shock._

_That girl was not the child she knew. Her hair and eyes were both darker. Her whole face was a different shape and her ears had something familiar about them. She was still a pretty little girl, there was no denying that, but she was not Elizabeth's little girl._

_The door to the bathroom opened and the last person Elizabeth wanted to see came out dripping wet with a towel around his waist. Elizabeth backed into the wall as she saw the face of Kolya. _

_Kolya saw the fear in her eyes and was immediately concerned._

"_Elizabeth what's wrong?"_

_He stepped forward to her but she stopped._

"_No, don't you dare come another step closer to me"_

_Kolya picked up Bree._

"_Darling go to your room"_

"_But Papa..."_

"_Honey Now"_

_He set Bree on the floor and she ran out of the room. Kolya took a few steps closer to Elizabeth and tried to encircle her in his arms but she fought back._

"_No, stay away"_

_Kolya didn't listen though and wrapped her in his arms, at which point Elizabeth started hitting him. _

"_Elizabeth calm down, you are safe. You were dreaming"_

_Elizabeth looked up at him and shook her head_

"_No, this is the dream"_

_Kolya brushed back the hair on her forehead and kissed her. _

"_Elizabeth I promise you. Sheppard can't get you. You're safe. You're both safe."_

_Elizabeth was sat on the sofa in Kolya's living room. She was perched on the edge ready to jump up if something didn't feel right. Kolya had managed to calm her down, but it didn't mean she trusted him. Something was very wrong._

_Hearing a noise Elizabeth spun round and saw Kolya come nto the room fully dressed and wearing a wry look on his face. Elizabeth was wearing a corset dress which was floaty at the bottom. Kolya came and sat next to her. When he did Elizabeth shifted along to the other side to be as far away from him as possible. _

_Kolya sighed and stood up. He began pacing around the room, Elizabeth could tell he was pissed._

"_Elizabeth. You do this every time and every time I tell you that he will never hurt you again."_

_Elizabeth looked up at him briefly._

"_What happened?"_

_Kolya shook his head and turned to her._

"_I will go though this for you again, but Elizabeth you need to stop doing this. We met with some people; Sora knew them well. They betrayed us. Then a few months later they came and abducted you. They brainwashed you and when I eventually found you, Sheppard had made you different. He'd made you into a killer. We found out a few months later that you were pregnant, with his child. I begged you to get rid of it, but you wouldn't. You kept saying that the child hadn't done anything wrong..."_

_Kolya stopped when Elizabeth shook her head._

"_No that's not right; that's not what happened"_

_Kolya sighed and sat down next to her. _

"_Elizabeth that's part of the programming you know that. It was a fail safe that Sheppard installed, he tried to make you doubt me, to doubt us"_

_Elizabeth stood up and walked to the far end of the room. She stared out of the window and sighed._

"_That's not true. John would never hurt me"_

_Elizabeth jumped as she heard something smash next to her. Turning round in shock she saw Kolya, his eyes full of anger._

"_Damn it Elizabeth."_

_Kolya looked at her, he could see the fear in her eyes and he immediately regretted what he had done. _

"_I'm sorry, Elizabeth I'm sorry."_

_Kolya sat down on the sofa and buried his head in his hands._

"_Please stop defending him. I know that when he brainwashed you he made you believe you were his wife but you're not. You told me that a part of you, the part that he created, loved Sheppard but you don't."_

_Elizabeth felt almost entranced when she walked over to the sofa and sat next to him. She almost believed him, she could feel herself wanting to believe him. _

_She felt his hand touch her cheek and turn her head to face him. _

"_Please believe me my Elizabeth. I would never do anything to hurt you."_

_Elizabeth could feel herself drawn to him. She could feel herself moving closer to him. He slipped his hand to the back of her neck and pulled her head closer to him. _

"_Just forget about him Elizabeth"_

_As their lips touched, Elizabeth heard a loud smash and felt a sharp pain in her hand. She looked down and saw blood pouring down from it, shards of glass buried into her palm_

Elizabeth looked up into the mirror of her Atlantis bathroom. The mirror that used to hang on the wall was no longer there, the glass sat in the sink with some shards buried in her hand.

Time seemed to move slowly as she tried to pick the biggest shards out of her hand. She only stopped when she felt someone stand behind her and switch on the bathroom light.

John was broke out of his peaceful sleep when he heard a noise from the bathroom. Looking next to him, he could see Bree lying peaceful where she had fallen asleep but the space where Elizabeth had fallen asleep was vacated. Slowly rising from the bed, careful not to wake Bree he walked to the bathroom and switch on the light. As soon as the light flooded the bathroom he could see the broken mirror.

He looked over Elizabeth's shoulder and saw the blood pouring from her hand.

"Elizabeth?"

She turned round to him, tears falling from her eyes.

"It happened again"

John carefully wrapped Elizabeth in his arms being careful not to knock her hand.

Five minutes after Elizabeth had stopped crying John had called for the night doctor, which just happened to be Carson. When he arrived in the room Bree was still sleeping peacefully and Elizabeth was sitting on a chair which John sat next to her smoothing down her hair. Carson walked over to her and saw the hand which was all cut up and bloody. Slowly he bent down in front of her and took her hand.

"How did this happened Elizabeth?"

Elizabeth brushed a piece of her hair from her eyes.

"I was...sleepwalking"

Carson was about to press but he received a look from John which told him to leave it alone.

It took Carson just a little over ten minutes to treat Elizabeth's hand and give her something for the pain and with an instruction to come and see him in the morning for stitches. She had than crawled back into bed next to Bree and fallen straight back to sleep.

After checking on Elizabeth and placing a kiss to her temple, he led Carson outside. Once in the corridor Carson turned to him.

"As that happened before John?"

John lent against the wall

"The first time it happened was about 2 months after I got back to Earth. She told me she'd had a dream about Kolya. It happens, maybe twice a year. After she dreams about Kolya. She never tells me what happens in the dreams though. It's almost like she's scared."

Carson nodded

"It's a form of self harm. She's doing it unconsciously but it's easing the pain"

John nodded

"I got rid of every mirror in our bedroom, but she'd just sleepwalk to the nearest mirror, sometimes it was the nearest knife. You have no idea how often I often it happened and every time it did her doctor thought it was domestic abuse. She tried getting Elizabeth to leave me at one point. The thing is that it stopped. About two years ago she stopped doing it. She was so happy and now all this has happened she's doing it again"

Carson nodded

"Did she ever see a psychologist about it?"

John shook his head

"She wouldn't go. I made appointments for her with the SGC shrink but she always found something to do at that exact time. There was one time when she did talk to the shrink but she stormed out and then hit me. She wouldn't tell me what had been said but it upset her enough to kick me into the spare room for a few nights."

Carson smiled at the thought of Elizabeth hitting John who was taller and physically stronger and patted John on the shoulder.

"Get some sleep lad. I'll talk to Kate and see if she'll have a little talk with Elizabeth"

John shook his head

"Don't bother she won't talk to her"

Carson smirked

"She doesn't have to know that Kate is planning to talk to her does she?"

John smiled and nodded

"I guess not"

Carson motioned his head to the door to John's quarters.

"Go get some rest"

John nodded

"You too"

John thanked Carson and than walked back into his quarters and over to the bed. He laid down next to Elizabeth and wrapped his arm around her waist and buried his head in the curls of her hair sighing deeply wishing he knew what had caused this.

Kolya's Temporary Quarters

Kolya sat cross-legged on the floor, his eyes closed tightly and his body relaxed. Suddenly he fell to the side and opened his eyes in shock. It hadn't worked. She'd brought herself out of it again, but this time the connection had been the strongest it had ever been before. The link was now direct and it was more likely to work. She was certainly being more responsive to his actions. It was working. Kolya smiled and climbed into the bed. A smirk plastered across his face.

Elizabeth woke up the next day to feel two tiny arms wrapping themselves around her. Elizabeth looked down and saw Bree yawning.

"Good Morning Mummy"

Elizabeth kissed her forehead and held her tightly. As she did she felt a sharp pain in her hand. She looked down at it and saw the bandage wrapped around it, she could see the bloody seeping through and she remembered what had happened the night before.

Without Elizabeth realizing Bree had moved behind her and jumped onto John.

"Hi Daddy"

John kissed her forehead and pulled her onto his chest like he used to do when she was a baby. John stood up with Bree and carried her into the conjoining room which held Bree's things and left her to get changed. He than walked back over to Elizabeth and kissed her cheek.

"How are you this morning?"

Elizabeth sat up and turned to him.

"I don't know"

John grabbed her hand.

"I'm going to take Bree to get some breakfast. Do you want to come?"

Elizabeth shook her head

"No, No I'm going to get this bandage changed and get my stitches but I'll come afterwards.

John nodded, kissed her once more and than headed into the bathroom.

Elizabeth headed into the infirmary and walked over to Carson's office. She knocked on the door and Carson waved her in.

"What can I do for you love?"

Elizabeth held up her bandaged hand.

"I came for the stitches"

Carson nodded

"Of course"

Carson stood up, led her into the main part of the infirmary, sat her down on one of the beds, and started working on her hand.

"How are you feeling this morning?"

Elizabeth smiled.

"I'm fine, thank you"

Carson nodded and smiled at her.

"Good"

Carson finished stitching up her hand and smiled at her

"All done. Where you heading now?"

"Mess Hall."

Carson smiled while Elizabeth thanked him and stood up. When she was out of the infirmary, Carson contacted Kate and told her where Elizabeth was heading.

Elizabeth was walking through the corridors, half lost in her thoughts when she bumped into someone.

"Oh I'm sorry"

She looked down at the person, which she had just bumped into. It was a teenage boy about 15 maybe 16 years old, obviously Athosian, he was good looking and just a little smaller than Elizabeth. He looked up at Elizabeth and broke into a smile

"Dr Weir, it's good to see you again"

Elizabeth tried furiously to remember who this boy was and than it came to her.

"Jinto?"

He nodded

"You've grown so much. It's good to see you again"

Jinto nodded

"It's good to see you."

Jinto stood for a moment contemplating what to say

"I heard about what's been happening. I heard why you're back. How's Bree?"

Elizabeth nodded

"She's okay. She hasn't met him yet...but she will...probably today."

Jinto nodded and Elizabeth smiled at him

"Anyway what are you up to?"

Jinto shrugged

"There's a group of us that are being trained by Ford and Stackhouse, it's fun but I like being taught science more. Rodney teaches me, he says I'm insufferable sometimes."

Elizabeth smiled

"He doesn't mean it. He's probably just scared that you're smarter than him"

Jinto smiled at the compliment.

"Thanks for saying so but I doubt that's true."

Elizabeth smiled

"Don't sell yourself short"

Jinto smiled and the two continued to speak for a little longer until Kate came round the corridor interrupting them.

"Dr Weir"

Elizabeth turned to hear and smiled

"Kate"

The two women hugged and Jinto excused himself to give them a chance to talk.

"How are you settling back in?"

Elizabeth smiled

"It's amazing how right being here feels"

Kate smiled

"You've been missed, all of you have."

Elizabeth nodded

"We've missed Atlantis"

Kate took Elizabeth by the arm.

"Come with me"

Kate led Elizabeth to a nearby balcony and Elizabeth looked over the edge into the ocean which she missed dearly. She than turned to Kate and lent against the railings.

"What can I do for you Kate?"

Kate crossed her arms.

"I just wanted to speak with you. I heard about what happened last night. I just wandering if you wanted to talk about it"

Elizabeth shook her head

"Well I don't"

Elizabeth went to leave when Kate called to her

"It's not the first time it has happened, is it?"

Elizabeth turned back to her.

"John told you?"

Kate shook her head

"No and it doesn't matter how I heard, all I want to do us talk with you about this. Try and help you though it"

Elizabeth ran a hand through her hair.

"Kate, I appreciate that you want to help me, but I can not talk about this. I don't want to think about it"

Elizabeth left Kate standing on the balcony while she went to the mess hall.

Elizabeth spotted John sitting in the far corner next to the balcony, Bree was sat on his lap with Aiden and Rodney sitting opposite them.

Elizabeth walked over to them smiling at Aiden and Rodney before turning to John.

"Can I have a word with you? In private"

John nodded and stood up, placing Bree in the chair he had just vacated before following Elizabeth to a nearby balcony.

"What's wrong?"

Elizabeth looked up at him

"I would prefer it if you didn't discuss my emotional state with a shrink"

John took a step forward.

"Look, I told Carson last night that it has happened before, he said he'd ask Kate to talk to you"

Elizabeth threw her arms up in disbelief

"Carson knows? Dear God John why not just sky write it so the entire city knows that I spent nearly two weeks in a psychiatric unit because my doctor thought I was trying to kill myself"

Elizabeth breathed deeply and lent against the railing. John walked over to her.

"I didn't tell him that Elizabeth. I told him what we agreed. I told him that you never talked to a shrink. I told him that the doctor thought that I was abusing you and to be honest you she think that to begin with. I never told him about what you went though"

Elizabeth buried her head in her hands.

"That was the worst two weeks of my life. People kept thinking I was crazy. If it wasn't for Carolyn pulling some strings I would have been there longer."

John moved forward and wrapped her in his arms.

"It doesn't matter now Elizabeth."

Elizabeth nodded and looked up at him

"But John why is it happening again. I thought I was over it"

John caressed her cheek.

"Hey, it won't happen again I promise you"

Elizabeth nodded and buried her head in his chest

"I hope to God you're right"

TBC...


End file.
